>input_sequence_70200
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---------------------------AAGACCACCTAATCTCTCTCTCTAATCCGAAACCAGAGGCAGCGCCGGAAGCA
GCAGCGGCAGTAGCTAGCGACACACAACAACTACAGCAAGCACACG---GGAGGAGGAAGAAGAAGGCTCTGCAGTTCTA
CACTTCTAC-TTCTGCACGCATGGGGAACTGCGCCATCACGCACCAGGCCACCTCGTGGGCGGACGACGGCGAGTGGGAG
CTGCCGTCGCCCGGCGACGAGGACGAGGGGCAAGCGGAGCAGAGGAAGGAGCACGTCAGCGAGGTGACCATCAGGATCAG
CAAGCGGCAGCTGCAGGAGCTGGTGGACAAGAGGGCCGACGACGGCG------------TCTGGAAGGGCCGGCGGTCGG
CGTCGGAGCTTCTGACGGACATCATGAACGCCGGGGAGGTGCACCACCACGTCGACCACTGCAGGGCGGCGCACTGGAAG
CCCGCTCTGCAGAGCATCCCGGAGGCGGTGGAGTCGTGACGCTACGCCCAGTGACGCGTCCCGGCCATGGCTTTCGATCG
CCGGGTTTGGGCTTCTCGTCTCCTTCTTGGTTGCTTCTTCGCCGTGTCGACCTTTGGTAGAACACACAGCTTTTATGCGG
CCTTTTTGTGTTATTATTCTTTGGTTTGGATCCAACGAACAATGTATATA------------------------------
----------------------------------------------------GTAGGGAAAGT---------------GG
TGATGTAAATTGTAAAGTAGATCAATGTTCTTCTGTCCATACGGCTTTTTGTGTGTGGAACAA------ACCAAGCATTC
TCAG----------------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G320400
ACCGGACGGCGATCACGAGACGAGCCAGCACGACCAGACAGCTTTCCTGCCACCAATGATAAGTGGCGCA----CTCGCG
GATATAGCTCGCATGTCCCATCCATCTCCCGGCCCCGGAGTGCGATTTCACACAAGGCGGCATCATGATTGCGTTTCTTC
GAGGCTACGGCAAATATTTCCACTTGCGAACGTATTACGTACTTAATTTGCATCTCCAGCTATGCTCGGCAGCAAGTAGT
TGACGGTTGGCCGTTGCATCAAGTATAGTGATTGTTGTTCTCTCAA----------------------------------
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------------------------------------------AAAAAAAAGTATAGTGATTGTTCAAGA-----------
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----------------------------TAATTAACTCGAACTGTTTCATGTAAATAAATAAATCCA------------T
GTATAGTGATTGTGCAAGATAGCGTCAACCGCAAAACGATGTGAGGCCGCCGACGGGCATGTGTCACCGCGATGCATGCA
ACCTGCACGCGACCAACGTGACGGCCGCTCAACAAGAGGAGGAACCGCGACAGCCGCCAACAGGGTGCGTCCAAAACCGC
GGAATTTGCAGCTCACCGCCCACAAGCATTGGCGGCTTGGCGCTGTCATCTGTCCGACACGAATATACAAAGCGCACAGC
GACGCGCCGAAGGCGCCGAGCCTGCGGCCAGGCGTGCACCGACGAGGCGCCGGGCGCACAGCACGCGGCCACGACACCGC
GACCTCATCGACCACGACGCCTCCCTCCAACCGCCGCGGCTAAGCAATGCCA-----GCCACCGGGGCGGTGAGCTGCAG
GGGAAAGAATCCGCTGGAAAAAGCCGCGTTCCCACCGCGAGCGC-----------CCATGCGAGATCCCGCGCCCCCCCG
CGTTCCCACTCGTCCCACCCACTCGTAACCATCCGCCACGGCGCCCACGTAGGATTCGATCCCCCCACGTCAGTGTCCAG
CGCGGCCGATACGTCGGCTGCGGCTTTTGCCCGGACGGTACTGCCACCCCCGTTCGCTCCAAGCCTCCGACTATATATCC
GCACCTCTCAGACCAGCTGGTCACACAAAGACCACCTAATCTCTCTCTCTAATCCGAAACCAGAGGCAGCGCCGGAAGCA
GCAGCGGCAGTAGCTAGCGACACACAACAACTACAGCAAGCACACG---GGAGGAGGAAGAAGAAGGCTCTGCAGTTCTA
CACTTCTAC-TTCTGCACGCATGGGGAACTGCGCCATCACGCACCAGGCCACCTCGTGGGCGGACGACGGCGAGTGGGAG
CTGCCGTCGCCCGGCGACGAGGACGAGGGGCAAGCGGAGCAGAGGAAGGAGCACGTCAGCGAGGTGACCATCAGGATCAG
CAAGCGGCAGCTGCAGGAGCTGGTGGACAAGAGGGCCGACGACGGCG------------TCTGGAAGGGCCGGCGGTCGG
CGTCGGAGCTTCTGACGGACATCATGAACGCCGGGGAGGTGCACCACCACGTCGACCACTGCAGGGCGGCGCACTGGAAG
CCCGCTCTGCAGAGCATCCCGGAGGCGGTGGAGTCGTGACGCTACGCCCAGTGACGCGTCCCGGCCATGGCTTTCGATCG
CCGGGTTTGGGCTTCTCGTCTCCTTCTTGGTTGCTTCTTCGCCGTGTCGACCTTTGGTAGAACACACAGCTTTTATGCGG
CCTTTTTGTGTTATTATTCTTTGGTTTGGATCCAACGAACAATGTATATA------------------------------
----------------------------------------------------GTAGGGAAAGT---------------GG
TGATGTAAATTGTAAAGTAGATCAATGTTCTTCTGTCCATACGGCTTTTTGTGTGTGGAACAA------ACCAAGCATTC
TCAGTCGATCTGCTGCTTTGTGCGCG------GAACAAACCAAGCATTTTTCACTTGATCTGCTGTCCAGAAACACGGTA
CAGACGAGCTTACCAGGAAGAGGAGGAAGAAGAAACCTACAAGGGACCAT--------------------------GGCC
AAACTTGGAAACAGATGAGA----------------A----------------TGCCCTGCAGGGCTGCAAAGCAATGTT
GGTTGGTTGAACCCAGAAGCCAGGTTATGTTCCACTCAAAAAAAGAAAAGAAAAAAGAATCCAGGTTATGCAATGT----
--AATTATGAATCATTGGGTGTGATCTGCCCAGTAAAGTCGTGGGTACCAT-----------------------------
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-------------------TACCAATGAAGATTGCACACATGCATTTTCTTTCCTCCACGTTCATAAGCCCGTGCATTAA
AAATGGGCAGTCTTGGTTCG-TTCGCCTGCCGCGAGATGCATGAAAGACCTGATTCGCTATTATACTAGGATTTTACGAT
TTATTAGAAATCACCTCACCTAATAATATTACAAAAATACTACTACTATGTATTAGAAATACTGGTAGAGTGGACTTCTC
GACATCTGACTTCCTTTTGTGTAGTATTTAATCAGGCTACACAATCAAGGAGGTTACAACAATAAAAAATACAAAAATGA
TA--GAGCAGATTTGGATTAGGGGGGCCAAGTGCTATTAAAATAGGTTTAGGAGGGCCAAACCTTAAGCAAATACTCCCT
CCGTTCCTAAATATAGGGTGTATAGGTTTACCAGCACCACTCACATGGGGCCGAGACCATGTACACATGCTCGAGCTCCC
ATGACACATAGAACCAAAACTGAAAGTGATTATAGTTCCATCATCCAGAGGAGCACACAATAGCAATATTACTTAGTGCC
AAAGTGTAACTTCTTCCATGGACACATGAGGCTTATCAACGGTACTATCCCTATGGACTGGTCTAGAGCAGCCCACATTC
ATAAGGTGGCGAAGAGGACGGTTGGGGTTCTTCCTGACCACTGTGCCGCATAAGGCCACATGGTCCAAGCACCTTGTTGC
CCCTA
>chr3B_1
ACCGGACGGCGATCGCGAGACGAGCCAGCACGACCAGACAGCTTTCCTACCGCCAATGATAAGTGGCGCACTTGCTCGCG
GATATAGCTCGCGCGTC----CCATCTCCCGGCCCCGGAGTGCGATTTCACAGAAGGTGGCATCATGATTGCGTTTCTTC
GAGGCTACGGCAAG-ATTTCCACTTGCGAGCACGAA------TTAATTTGCATCTCCAGCGATGTCCGGTAA----CAGT
TGACGGTTGGCCATTGCATCAGGTAGAAGTAATTAATTATGGGTCACGCTAACTGCCACACGTGTGGCAGGAAGGAAAAC
GCACCACACGTCTTTAATGTAAACAGATTGTCACGTCATTGCATGCATGCATGCAGGAATCTTTTTGGATTTTCAATTTT
TAAAATGTTTTATCTCTTAATCGAAAAATCCGATTGAAAATCCGTTTTCACCATTAAATCCCTCGCGATGAGATCTTCGA
AACTAGATCCACATGTTGATATGTTTTGATGAATTTTTTTTTGGATTAAAAGTTGCCATGTCTATTGCATATGAATTGTC
ATGATGTTTACACTGAAGTTGCCATGATATGTTTCAGCTATTTTCTTCTACATTTAAAAGTAATTTTTGACATTTATAAA
ACGGGGAATTAAGAAACTAGACTTGCCATGAACCATAAACTAAAATTATCATGATACATGCACGTAAAATTGCCATGGTT
TATACAAAAAATAATTTTCATGATCAAAGTATTGGAGTTGCCATCATCAAAATACTAAAATTGCTATGATCTACAAACTA
AAATTGCCACATGGCAATTTTAGTTTAAGCCCTATGGCAACTGCAGTGTAAACATCGTGGCAACTTCTGGTAAAAAAAAT
CGTCGAAACATATCAACATGGGGTCTAGTTTTGAAGATCTCGTCGAGACGGATTTAATGGTGAAAACGGATTTTTAGTTC
GCTTTTTTGTTTAGGAGATACAACATTTTTAAGCCGAAAACCAAAAAAAATTCTACTGATGTCATCTATTCATACGTGGC
AAAATGAGTCGTGATGGAGGCATGTGAGCGATGTGCAAACATCCACACGTGTGGGCGTTAACATTTCCATTAATTATATA
ACTCCTCGCAAAATAATACAGTAATAATTAATTAACAACTTGAACGTGGCTCCTGTAAATAAATCCA------------T
G--TAGTGATCGTGCGAGATAGCGTCAACTGCGAAACGATGTGAGGCCGCCGACAGGCATGTGTCACCGCGATGCATGCA
ACCTGCACGCGACCAACGTGATGGCCGCTCAACAAGAGGAGGAACCGCGACAGCCGCCAACAGGATGCGTCCAAAGCCGC
GGAATTTGCAGCTCACCGCCCACAAGCATTGGCGGCTTGGCGCTGTCAGCTGTCCGACACGAATAAACAAAGCGCACAGT
GAGGCGCCGAAGGCACCCAGTTTGCGGCCAGGCGTGCACCGACGAGGCGCCGGACGCACAGCACGCGGCCACGACACCGC
GACTTCATCGACCACGACGGCTC---CCAACCGCCGCGGCTAAGCAATGCCATGCCAGCCACCGGGACGGTGAGCTGCAG
GAGAATCCGCT-----GAAAAAGCCGCGTTCCCACTGCGAGCGC-----------CCATCGCAGATCCCGCGCTCCCCCG
CGTTCCCACTCGTCCCACCCACTCGCAACCATCCGCCACGGCGCCCACGTAGGATTCGAT--CCCCACGTCAGTGTCCAG
CGCGGCCGAAACGTCGGCTGCGGCTTTTCCCAGGACGGTACTGCCACCCCCGTTCGCTCCAAGCCCCCGACTATATATCC
GCGCCTCTCAGACCAGCTGGTCACACAAAGACCACCTAATCTCTCTCTG--ATCTGGAAGCAGAGGCAGCGCCGGAAGCA
------GCAGCAGCTAGCGACACACAACAACTACAGCAAGCACACAGC---AGGAGGAAGAAGAAGGCTCTGCAGTTCTA
CACTTCTAC-TTCTACACGTATGGGCAACTGCGCCATCACGCATCAGGCCACGTCGTGGGCGGACGACGGCGAGTGGGAG
CTGCCGTCGCCCGGCAACGACGACGAGGGGCGCGCGGAGCAGAGGAAGGAGCACGTCAGCGAGGTAACCATCCGTATCAG
CAAGCGGCAGCTGCAGGAGCTGGTGGACAAGAGGGCCGCCGACGACGGGCACGGTCACATCTGGAAGAGCGGGCGGTCGG
CGTCGGAGCTTCTGGTCGACATCATGAACGCCGGGGAGGTCCACCACCACGTCGAGCACTGCAGGGCGGCGCACTGGAAG
CCCGCCCTGCAGAGCATCCCGGAGGCGGTGGAGTCGTGACGCTACGCCCAGTGACGCGTCCCGGCCATGGCTTTCGCCGG
GC----TTGGGTTTCTCCTCTCTTTCTTGGTTGCTTCTTCGCCGTGTCTTTTGTTAGA-----ACACAGCTTTTACGCGG
CCTTTCTGTGTC---ATTCTTTGGTTTGGATCCAACGAACAATGTATATTG-----------------------------
----------------------------------------------------GTAGGGAAAGTGGTGATACACACCACGG
TGATGTAAATTGTAAAGTAGATCGATGTTCTTCTGTCCATACGGCTTTTTGTGTGTGGAACAA------ACCAAGCATTC
TCAGTTGATCTGCTGTTTTGTGTGTGTGTGTGGAACAAAGCAAGCA-TTTTCACTTGATCCGCTGTCCAAAAACACAGTA
CAGACGAGCTTACCAGGAAGAGGAGGAAGAAGAAACCTGCAAGGGACCAT--------------------------AGCC
AAACTTGGAAACAGATCAGA----------------ACAGAAGCGATTCCATATGCCCAGCAAGGGCTGCA---------
----------------AAGCCAAGTTATGTTCCACTAAAAAAAA----------------CCAAGTTATGCAATGT----
--GATTATGAATCATTGGGTATGATCTTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNGGTACCAACGAAGATTGCACACATACATTTTCTTTCGCCCACGTTCAGAAGCCCTTGCATTAA
AAATGGGCATTCTTGGTTCGTTTCGCCTGCCGCGAGAGGCATGAATGACCTTATTCGCTATTGTTTTAGGATTTTAAACG
ATTTAAGAAATCACCTCACCTAACAATATTACAAAA-------TATTACGTGTTAGAAATACTAGTAGAGTGGACTTCTC
GACTTCTGACTTCCTTTTGTGTAGTATTTAATCAGGCCACACAATCAAGGAAGTTACAACAAAGGAAAACACAAAAATGA
TACTGAGCAGATTTGGATTAGGGTGGCCAAGTGCTACTAA----------------------------------------
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>chr3A_1
ACCGGGCGACGATCACGAGACGAGCCAGCACGACCAGACAGCTTTCCTACCGCCAATGATAAGTGGCGCACTTGCTCGCG
GATATAGCTCGCGCGTC----CCATCTCCCGGCCCCGGAGTGCGAGTTCACAGAAGGCGGCATCATGATTGCGTTTCTTC
GAGGCTACGGCAAC-ATTTCCACTTGCGAGCACGAA------TTAATCTGCATCTCCAGCTATACCCGGTAGCATGCAGT
TGACGGTTGGCCGTTGCACCAAGTATTAATAACTATTTTCGC---A----------------------------------
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------------------------------------------AAAAAAAAGTAGGAGTGC--------------------
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-------------------------AATTAATTAACTCGAACTGTCTAATGTATACTACTAAATAAATAAGTAAATCCTT
GTATAGTGATTGTGCAAGATAGCGTCAACCGCAAAACGATGTGAGGCCGCCGACGGGCATGTGTCACCGCGATGCATGCG
ACCTGCACGCGACCAACGTGATGGCCGCTCAACAAGAGGAGGAACCGCGACAGCCGCCAACAGGGTGCGTCCAAAACCGC
GGAATTTGCAGCTCACCGCCCACAAGCATTGGCGGCTAGGCGCTGTCATCTGTCCGACACGAATAAACAAAGCGCACAGC
GACGCGCCGAAGGCACCCAGTTTGCGGCCAGGCGTGCACTGACGAGGCGCCGGACGCACCGCACGCGGCCACGACGCC--
---------------------TC---CCAACCGCCGCGGCTAAGCAATGCCACGCCAGCCACCGGGGCGGTGAGCTGCAG
GAGAATCCGCT-----GAAAAAGCCGCGTTCCCACGGCGACCGTCCGGGCCCCGTCCATGCGAGATCCCGCGCTCCCCCG
CGTTCCCACTCGTCCCACCCACTCGCAACCATCCGGCACGGCGCCCACGTAGGATCCCAT--CCCCACGTCACCGTCCAG
CGCGGCCGAAGCGTCGGCTGTGGCTTTTGCCCGGACGGTACTGCCACCCCCGTTCGCTCCAAGCCTCCCACTATATATCC
GCGCCTCTCAGACCAGCTGGTCACACAAAGACCACCTAATCTCTCTCTCTAATCCGA---------------CGGAAGCA
------GCAGCAGCTAGCGACACACAACAACTACAGCAAGCACACAGCAGGAGGAGGAAGAAGAAGGCTCCATCTATCTA
TACTCTATAGTTCCACACGCATGGGGAACTGCGCCATCACGCACCAGGCCACGTCGTGGGCGGACGACGGCGAGTGGGAG
CTGCCGTCGCCGGG---CGACGACGAGGCGCACGAGGAGCGGAGGAAGGAGCACGCCAGCGAGGTGACCATCCGGATCAG
CAAGCGCCAGCTGCAGGAGCTGGTGGACAAGAGGGCCGACGACGGCG------------TCTGGAAGGGCCGGCGGTCGG
CGTCGGAGCTTCTGGCGGACATCATGAACGCCGGGGAGGTGCACCACCACGTCGACCACTGCAGGGCGGCGCACTGGAAG
CCCGCCCTCCAGAGCATCCCGGAGGCGGTGGAGTCGTGACGCTACGCCCCGTGACGCGTGCCGGCCATGGCTTTCGATCG
CCGGGTTTGGGTTTCTCGCCTCTTTCTTGGTTGCTTCTTCGCCGTGTCT---------------CACAGCTTTTTGGCGG
CCTTTTTGTGC---TATTCTTTGGTTTGGATCCAACGAACAATGTATATACTCTCCGTTCCAAAATAGATGACCCAACTT
TATACTAAGGTCAGTACAAAGTTGGGTCATCTATTTTGGAACGGAGGGAGTAGTAGGGAAAGT---------------GG
TGATGTAAATTGTAAAGTAGAT----GTTCTACTGTCCATACGGCTTTTTGTGTGTGGAACAACAACAAACCAAACATTC
TCAGTTGATCTGCTGCTTTGTGTGTG------GCACAAACCAAGCA-TTTTCACTTGATCCGCTGTCCAAAAACACGGTA
CAGACGAGCTTACCAGGAAGAGGAGGAAGAAGAAACCTACAAGGGTGCAAAGCAATGTTGGTTGGTTGAACCCAGAAGCC
AAACCTGGAAACTGATGAGGACAGAAGCGATTCTGTA----------------TGCCCTGCAAGGGTGCAAAGCAATGTT
GGTTGGTTGATCCCAGAAGCCAAGTTATGTTCCACTAAAGAAA------------------CAAGTTATGCAATGTAATT
ATGATTATGAATCATTGGGTGTGATCTGCCCTGTAGAGTCGTGGGTACCAATGAA-------------------------
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--------------------------GAAGATTGCACATATGCATTTTCTTTCCTCCACGTTCAGAAGCCCGTGCATTAA
AATT-GGCATTCTTGGTTCG-TCCGCCTGCCGCGAGAGGCATGAAAGACCTGATTCGCTATTATATTAGGATTTTACGAT
TTATTAGAAATCACCTCACCTAATAATATTACAAAAATACTA-TACTATGTATTAGAAATACTGGTAGAGTGGACTTCTC
GACTTCTGACTTCCTTTTGTGTAGTATTTAACCAGGCTACACAATCAATGAGGTTACAACAATCGAAAAAACAAAAATGA
TA--GAGCAGATATGGATTAGGGGGGCCAAGTGCTATTAAAATAGGCTGGGGAGGGCCAAACCTTAAGCAAATACTCCCT
CTGTTTCAAAATA-------------------------------------------------------------------
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>SNPs
------------------------------------------------S--S----------------------------
------------SS---SSSS-------------------------------S---------------------------
-------------SS--------------S-SSSSSSSSSSS-----------------------S---S----S-S---
---------------------------SSS-S-SS-S---S-SSS-----------------------------------
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-------------------------------------------------------S----SSSSSSSSS-----------
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---------------------------------------------S-S-----S--------------------------
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---------------------S----------------------------------------------------------
-----------------------------------------------------------------S--------------
--------------S--S--SS-------------------------------S--------------------------
---S---------------S---SSS------------------------------------------------------
-S---SSSSSSSSSSS-------------------S-------------------------------------S------
-------------------------S----------------------------------SS------------------
---------S----------------------------------------------------------------------
--S--------------------------------------------------------S--------------------
SSSSSS----S----------------------------------S----------------------------------
--------------S-------------------------------------S---------------------------
---------------S----S-----------S---------------------------------------S-------
--------------------------------------------------------------------------------
--------------S-----------------------------------------------------------------
-----S--------------------------------------------------------------------------
-----------S----------S-------------------------SSSSS--S-SSSSSS------------S----
-----------SSS------------------------------------------------------------------
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-----------------------S--------------------------------------------------------
-----S----------------S-S---------------------S-------------S--------S----------
----------------------------------------------------------------------------S---
--------------------------------------------------------------S--S--------------
----------S-----------S-------------S-------SSSSSSSSSSSSSSSS---S----------------
--S----------------------------S---S--------------S-----------------------------
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-------------------------S--------------------------------------S---------------
---------S---------------------------S---------------------------S--------------
------------------------------------------S-------------------------------------
---S-----------------------------------------------------------SS----S----------
----------------------------------------------S-SS------------------------------
-S---S-S-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS
>forward_1609
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---------------------------------------------------------------------GTGAGCTGCAG
GGGAAAGAA-----------------------------------------------------------------------
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>reverse_3944
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-----------------------GGGGTTCTTCCTGACCACTG-------------------------------------
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